Antigen

Antigen Class

TFs and others

Antigen

CTCF

Cell type

Cell type Class

Neural

Cell type

GBM8

NA

NA

Sample

source_name

low-passage glioma-initiating stem-like cells (GBM8)

cell type

low-passage glioma-initiating stem-like cells (GBM8)

chip antibody

CTCF (#3418, Cell Signaling)

treatment

treated with Pool of 4 siRNA against HOXD-AS2 for 48 hours

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7546S, NEB). ChIP-Seq with Drosophila spike-in chromatin (Cat. 53083, Active Motif) and Drosophila -specific histone variant, H2Av (Cat. 61686, Active Motif) were added to each sample prior IP for normalization.

Sequencing Platform

instrument_model

Illumina HiSeq 2500

hg38

Number of total reads

9810818

Reads aligned (%)

83.3

Duplicates removed (%)

13.0

Number of peaks

4814 (qval < 1E-05)

hg19

Number of total reads

9810818

Reads aligned (%)

82.2

Duplicates removed (%)

15.7

Number of peaks

4872 (qval < 1E-05)